R/countpeaks.R

In yufree/xMSanalyzer: xMSanalyzer: R package for data analysis, comparison, and annotation of metabolomics data.

#' countpeaks
#' 
#' Count the number of signals in the intensity vector.
#' 
#' 
#' @param intensity_vec Vector of intensities
#' @param missing_val How are the missing values represented in the intensity
#' vector? eg: NA or 0
#' @return Number of peaks with signals.
countpeaks <- function(intensity_vec, missing_val = 0) {
    
    if (is.na(missing_val) == TRUE) {
        zeroind <- which(is.na(intensity_vec) == FALSE)
    } else {
        if (missing_val == 0) {
            zeroind <- which(intensity_vec > 0)
        } else {
            stop(paste("Invalid value for \"missing_val\". Please use either \"NA\" or \"0\"", 
                sep = ""))
        }
    }
    
    
    return(length(zeroind))
}